I don't know what your plans are for the game (like if you want to keep it just as an arcade game for coffee breaks), but I'm imagining a grand campaign involving big scrolling maps in all directions, land, different controllable ships each with their own turn rates, armor levels, and different armaments, and a colossal story about finding another commando ship that has gotten stranded in enemy territory (or whatever you want! Alien ships, etc.).

The 30+ levels (which would then need save states to save and load progress) would have various land layouts (islands with bridges, chokepoints, and such), maybe text dialogue from characters, and a different scenario per level like escort missions (protecting a fragile ship or group of ships on a fixed route from enemies trying to destroy them). Submarines (with radar pinging) and aircraft come to mind.

There is a lot you can do with what you've got going, and I'd be interested in possibly supplying music and sound effects too.

EDIT: On top of the Story mode, you could also create a Skirmish mode with randomly generated land and an enemy fleet to destroy with your own allies (all with sliders on size of either fleet or arsenals given, to make the match as easy or as hard as players want). Multiplayer online combat or co-op is also a possibility (or hotseat on the same computer, with adjustable keyboard controls). Maybe you could build a level editor for people to just make their own stories and series of levels through. There's no limit!

After reading this again, some of the ideas you mentioned, especially about the customizable missions and storyline, I was reminded of Endless Sky, a great open source space-themed game. You might enjoy this, as it even has some of the mission types you mentioned, including escorts and battles where you attempt to destroy an enemy fleet.